The sandwich ELISA (sELISA) targeting sarcoplasmic calcium binding protein (SCP) is significantly influenced by food matrices, yet the mechanisms are unclear. To clarify the comprehensive effects of environments, matrices, and processing, SCP treated with diverse temperatures, pH, and matrices was subjected to ELISA, electrophoresis, multispectroscopic and molecular simulation assays. Recoveries of sELISA and indirect competitive ELISA (icELISA) were inhibited above 80 °C and 100 °C due to the unfolding of SCP. Under acidic conditions, SCP became more compact improving icELISA while reducing sELISA. The tertiary structure, aggregation state of SCP, and ELISA results were primarily impacted by inorganic salts, carbohydrates, and peanut oil via non-covalent interactions. Slighter impacts of processing on icELISA suggested SCP might preserve epitopes maintaining antibody recognition. These findings elucidated the effects of various factors on SCP structure and the mechanisms behind variations in ELISA results, additionally demonstrating the stronger interference resistance of icELISA.